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GitHub - bioinformatics-ua/gto: The genomics toolkit

 5 years ago
source link: https://github.com/bioinformatics-ua/gto
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README.md

Build Status Codacy Badge License: MIT

GTO

The genomics toolkit

INSTALL

Get GTO and make the project, using:

git clone https://github.com/bioinformatics-ua/gto.git
cd GTO/src/
make

Note, an already compiled version of GTO is available for 64 bit Linux OS in the bin/ directory.

GTO Programs

The GTO provides pipe support for easy integration with the majority of the tools. These include programs to shuffle, transform, simulate, compress, vizualize, among others. The GTO includes the following tools, divided by genomic data format type.

1. FASTQ tools

1.1 gto_fastq_to_fasta
1.2 gto_fastq_to_mfasta
1.3 gto_fastq_exclude_n
1.4 gto_fastq_extract_quality_scores
1.5 gto_fastq_info
1.6 gto_fastq_maximum_read_size
1.7 gto_fastq_minimum_quality_score
1.8 gto_fastq_minimum_read_size
1.9 gto_fastq_rand_extra_chars
1.10 gto_fastq_from_seq
1.11 gto_fastq_mutate
1.12 gto_fastq_split
1.13 gto_fastq_pack
1.14 gto_fastq_unpack
1.15 gto_fastq_quality_score_info
1.16 gto_fastq_quality_score_max
1.17 gto_fastq_quality_score_min
1.18 gto_fastq_cut
1.19 gto_fastq_minimum_local_quality_score_forward
1.20 gto_fastq_minimum_local_quality_score_reverse
1.21 gto_fastq_clust_reads

2. FASTA tools

2.1 gto_fasta_to_seq
2.2 gto_fasta_from_seq
2.3 gto_fasta_extract
2.4 gto_fasta_extract_by_read
2.5 gto_fasta_info
2.6 gto_fasta_mutate
2.7 gto_fasta_rand_extra_chars
2.8 gto_fasta_extract_read_by_pattern
2.9 gto_fasta_find_n_pos
2.10 gto_fasta_split_reads
2.11 gto_fasta_rename_human_headers
2.12 gto_fasta_extract_pattern_coords

3. Genomic sequence tools

3.1 gto_genomic_gen_random_dna
3.2 gto_genomic_rand_seq_extra_chars
3.3 gto_genomic_dna_mutate
3.4 gto_genomic_extract
3.5 gto_genomic_period

4. Amino acid sequence tools

4.1 gto_amino_acid_to_group
4.2 gto_amino_acid_to_pseudo_dna

5. General purpose tools

5.1 gto_char_to_line
5.2 gto_reverse
5.3 gto_new_line_on_new_x
5.4 gto_upper_bound
5.5 gto_lower_bound
5.6 gto_brute_force_string
5.7 gto_real_to_binary_with_threshold
5.8 gto_sum
5.9 gto_filter
5.10 gto_word_search
5.11 gto_permute_by_blocks
5.12 gto_info
5.13 gto_segment
5.14 gto_comparative_map
5.15 gto_xs
5.16 gto_geco
5.17 gto_gede

CITE

Please cite the followings, if you use GTO: J. R. Almeida, D. Pratas. GTO: the genomics toolkit, 2018.

ISSUES

Please let us know if there is any issues.

LICENSE

GTO is under MIT license. For more information, click here.


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